When connecting two switches, should I use normal switch ports or the SFP ports?

I have two 48 port gigabit Netgear switches with 2 SFP ports each (I also have two Mini-GBIC copper transceiver modules)

Is it best to set the ports up by using the built in ports (i.e. plug port 1 of switchB into port 48 of switchA and port1 of switchA into the router) or is there an advantage to using the Mini-GBIC?

(Let's call the SFP ports 49 and 50)

Router → port 49 on switchA, port 50 switchA → port 49 SwitchB

mini-GBIC seems to be simply a "let's add to the confusion" description of an SFP module. There's no shortage of available confusion, and at times I swear a good bit of it is deliberate.

For short-distance links on a gigabit switch (where all ports are Gigabit) it makes, no, zip, zero, nada, (etc) difference if you use SFP ports or wired ports to interconnect switches. SFP ports are primarily for allowing fiber connections over longer distances, when needed.

In the bad old days when you only had two or 4 gigabit ports, and those ports were the SFP slots, it mattered. With a full gigabit switch, it doesn't matter unless you have a 10GB uplink port (XFP or the other one I forget the acronym for just now.)

An SFP-copper module is not something you should waste money on buying, but if the money is already wasted, you can use it - it still makes no difference to the operation or effectiveness of the switch setup. If you don't need more than 48 ports (or 50, if you can use all 50 - many lock out a copper port when you use an SFP, but some don't), use one switch. If you don't need the full number of ports you'll have left on two switches after taking two ports to interconnect them, the best thing you can do for switching is to "trunk" multiple ports between switches - you have to set this up, you can't just plug in without setting up first - but you can have 2, 4, often up to 8 cables (removing up to 16 ports from your pool) to increase the traffic path between switches.

Other than keeping track of them, especially if setting up trunk groups, which port number goes where does not matter. For interswitch connections, it's usually less confusing to simply connect 48 to 48, 47 to 47, etc...Sometimes 48-24, 47-23 makes it easier to plug in other cables (not blocked by the switch-to-switch cables, if the switches are stacked in a rack with short cables.)

While there is no outward difference, depending on the model of switch, there may be a number of engineered hardware advantages to using an SFP port. However, IIRC Netgear does not make this type of information available as opposed to most enterprise switch vendors (even if they do sometimes make it hard to find).

Or, there may be no difference at all. Only the vendor can tell you this (or provide documentation that will tell you).

Here are some examples of how it may be different/better (not an exhaustive list):

1. The SFP ports may be less oversubscribed to the data plane than the copper ports. For instance, the SFP ports may not be oversubscribed at all, whereas with the copper ports you may be oversubscribed by 2:1 or worse.
2. The SFP ports may have more hardware buffers allocated to it than are allocated to the normal copper ports allowing for larger bursts of traffic before frames are dropped.
3. The queueing mechanism may be different on the SFP ports.

Keep in mind that many of these "small business" types of devices will use a "shared port" mechanism in which either the copper ports or the SFP ports can be used. In these cases, I would suspect there is little or no difference between the SFP port and the shared copper port (although other copper ports may be different).

This is what they are designed for, so I would use Mini-GBIC ports. Remember you probably need a crossover cable between the switches.

ADD: I expect it is RJ45 (category 5 cable) connectors, or use a regular port as you suggested.